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Thursday, October 08, 2009

Where are the CDK 1.3.1 and 1.2.4 releases ?!?

You might be wondering what is keeping the CDK 1.3.1 and 1.2.4 releases. And right you are. When we look at Supernightly, we get a clue (BTW, I hope the EBI nodes will join soon too):

Studying this table shows the reasons: there are too many regressions, too many failing unit tests. For example, 1.2.4 (while not yet released, called 1.2.3.git) has 50 new failing tests. Now, fair enough, this is mostly because of ioformats not being tested in 1.2.3 and most of the fails caused by a bug in the test, not in the code. But that still leaves 20 other failing tests. Mostly related to known bugs, and for some problems patches are actually available.

These last 22 we also see in the differences between 1.3.0 and 1.3.1 (while not yet released, called 1.3.0.git). That's because the ioformats modules is not tested in that branch either, pending a new merge with the cdk-1.2.x branch.

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This blog deals with chemblaics in the broader sense. Chemblaics (pronounced chem-bla-ics) is the science that uses computers to solve problems in chemistry, biochemistry and related fields. The big difference between chemblaics and areas such as chem(o)?informatics, chemometrics, computational chemistry, etc, is that chemblaics only uses open source software, open data, and open standards, making experimental results reproducible and validatable. And this is a big difference!

About Me

Assistant professor at the Dept of Bioinformatics - BiGCaT at NUTRIM, Maastricht University, studying biology at an unsupervised and atomic level. Open Science is my main hobby resulting in participation in, among many others, Bioclipse, CDK and WikiPathways. ORCID:0000-0001-7542-0286. Posts on G+ are personal.

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